To characterize electron-beam sensitive materials like zeolites, MOFs at sub-atomic resolution still faces challenges, dut to various of experimental limitations and obstacles. Electron ptychography is a potential candidate to solve these challenges and even break the resolution limitation of conventional transmission electron microscopy. In this work, we introduce 4D-STEM based ptychography to the beam-sensitive materials' characterization at sub-angstrom resolution, taking a zeolite, ZSM-5, as an example. After the systematic exploration on experimental parameters and optimization of reconstruction algrithms, we acquire the highest lateral resolution of this material and even in the zeolites family. Besides, the multi-slice reconstruction method enables us to obtain the electron-beam direction resolution. Based on these superiority of 4D-STEM ptychography, we are able to analyse the detailed structural and compositional inhomogeneity of ZSM-5 in three dimensions (3D), e.g., the 3D distribution of oxygen vacancies and the interface of MFI and MEL phases are investigated. 4D-STEM ptychography may open a new ero for high-resolution characterization of beam-sensitive materials under low dose.